Table 1.

Characteristics of the studies (n = 16) included in the systematic review.

Authors	Study-Period	Study Population	Ethnicity	Sample Type	Sequencing Platform	Main Results
Filardo et al. [24]	2016	Women with C. trachomatis (CT, n = 7), and healthy controls (HC, n = 7)	European	Endo-cervical swabs	V3-4 Illumina	CT women showed a marked increase in alpha-diversity indices (Shannon’s and Shannon-weaver’s) and an overall decrease in Lactobacillus spp., alongside an increase in anaerobic bacterial species, including G. vaginalis, A. vaginae, P. amnii, P. timonensis, and L. amnionii.
van der Veer et al. [14]	2013–2014	Women notified for C. trachomatis (CT) infection of sex partner (n = 93), of which n = 52 tested CT positive and n = 41 tested CT negative (controls)	European	Endocervical and/or Vaginal swabs	V3-4 Illumina	CT women were significantly associated with a cervico-vaginal microbiota characterized by diverse anaerobic bacteria or with a microbiota dominated by L. iners, as compared to a microbiota dominated by L. crispatus.
Balle et al. [18]	2013–2014	Women with C. trachomatis (CT+, n = 30), and uninfected controls (CT-, n = 42)	African	Endocervical and vaginal swabs	V4 Illumina	The endocervical microbiota diversity is not grossly altered in CT+ women, although CT+ women had higher relative abundance of G. vaginalis and other anaerobes, like Megasphaera spp., A. vaginae, Dialister spp., and Prevotella spp., all BV-associated bacteria, as compared to CT- women.
Ziklo et al. [15]	Not reported	Women with diagnosed C. trachomatis infection at baseline (CT-P, n = 11), with repeated CT infection in the last year (CT-RP, n = 3) and post antibiotic treatment (PAT, n = 13), as well as CT-negative controls (CT-N, n = 10)	Australian	Vaginal swabs	V3-4 Illumina	CT-P and CT-RP women were associated with elevated vaginal kynurenine/tryptophan ratios. CST-IV (anaerobic bacteria) showed significantly lower vaginal tryptophan levels as compared to CST-I (L. crispatus) and III (L. iners). In PAT women, a higher abundance of indole producing bacterial species were observed, including Porphyromonas asaccharolytica, Propionibacterium acnes, Fusobacterium nucleatum, Faecalibacterium prausnitzii, Enterococcus faecalis, Peptoniphilus harei, and Escherichia coli.
Tamarelle et al. [21]	2015	Women with C. trachomatis (CT+, n = 21), and uninfected controls (CT-, n = 111)	European	Vaginal swabs	V3-4 Illumina	CSTs were not significantly associated with C. trachomatis status but higher proportions of CT+ women were found in CST-III (L. iners) and CST-IV (anaerobic bacteria), rather than in CST-I (L. crispatus).
van Houdt et al. [19]	2008–2012	Women screened for C. trachomatis who tested negative at the first visit (n = 115). At subsequent yearly screening, n = 60 women tested CT-positive, and n = 55 women tested CT-negative (controls).	European	Vaginal swabs	V3-4 Illumina	Five CSTs were identified, four CSTs were dominated by Lactobacillus spp., of which L. crispatus (CST-I) and L. iners (CST-III) were the most common, and one CST was characterized by an array of strict and facultative anaerobes (CST-IV). Women with L. iners dominated CST-III had increased risk of CT infection.
Di Pietro et al. [29]	2016	Women with C. trachomatis infection (CT, n = 10), papilloma virus infection (HPV, n = 10), HPV/CT co-infection (n = 5), and healthy controls (HC, n = 10).	European	Endocervical swabs	V3-4 Illumina	Alpha diversity indices (Shannon’s and Shannon-weaver’s) were higher in either CT or HPV/CT co-infected women as compared to healthy controls. The cervical microbiota of CT positive and HPV/CT co-infected women was characterized by decreased Lactobacillus spp. and increased anaerobic bacterial species, like G. vaginalis, A. vaginae and A. christensenii. L. iners were also more frequently found in CT positive and HPV/CT co-infected women. By contrast, HPV positive women showed a similar microbiota to those in healthy controls.
Masha et al. [28]	2015	Pregnant women with Trichomonas Vaginalis (TV, n = 18), compared to pregnant women with C. trachomatis (CT, n = 14), and healthy controls (HC, n = 21)	African	Vaginal swabs	V2-4-8 Ion torrent PGM	Bacterial alpha-diversity indices (Simpson’s and Shannon’s) were significantly higher in women with either TV or CT as compared to healthy controls. Women with TV had increased abundance of Parvimonas and Prevotella spp. as compared to both CT+ women and healthy controls, whereas CT+ women had increased abundance of Anaerococcus, Collinsella, Corynebacterium, and Dialister spp.
Cheong et al. [27]	2010–2014	Women with C. trachomatis infection (CT, n = 42), and healthy controls (HC, n = 35)	Asian	Endocervical swabs	V3-4 Illumina	Women with CT infection showed no increased cervical bacterial alpha-diversity indices (Simpson’s, Shannon’s and Pielou’s). CT infection was associated to increased abundances of strict and facultative anaerobes, like Streptococcus, Megasphaera, Prevotella and Veillonella spp.
Ceccarani et al. [26]	2016	Women with bacterial vaginosis (BV, n = 20), vulvovaginal candidiasis (VVC, n = 18), C. trachomatis (CT, n = 20), and healthy controls (HC, n = 21)	European	Vaginal swabs	V3-4 Illumina	Alpha-diversity indices (Shannon’s and Chao1) were higher in BV women as compared to CT and HC women. Lactobacillus spp. were decreaed In BV, VVC and CT groups, while HC group microbiota was dominated by L. crispatus. In BV, VVC and CT, L. crispatus was replaced by L. iners. CT, BV and VVC, were characterized by anaerobes, such as Gardnerella, Prevotella, Megasphaera, Roseburia and Atopobium spp. The decrease of lactate was considered as a common marker of all the pathological conditions.
Filardo et al. [25]	2017	Women with C. trachomatis infection (CT, n = 42), and healthy controls (HC, n = 103).	European	Endocervical swabs	V4 Illumina	Alpha-diversity indices (Shannon’s and Shannon–Weaver’s) were significantly higher in CT women as compared to HC. CT microbiota was dominated by anaerobes (CTS-IV), and a specific network of G. vaginalis, P. amnii, P. buccalis, P. timonensis, A. christensenii and V. guangxiensis was identified as potential biomarker of CT infection. CT was also significantly correlated with increased levels of lactoferrin, IL-6, IL-1α, IFN-α, and IFN-β, whereas very low levels of IFN-γ were observed.
Borgogna et al. [17]	Not reported	Women with C. trachomatis infection (CT+, n = 54), CT/Micoplasma genitalium co-infection (CT+/MG+, n = 14), and healthy controls (HC, n = 77)	African-American	Vaginal swabs	V3-4 Illumina	Women with CT infection or coinfection CT/MG were associated with a CST-IV microbiota, characterized by decreased Lactobacillus spp. Significant differences in vaginal metabolites were identified in CT+ or CT+/MG+ women as compared to uninfected women, before and after adjustment for CSTs, with significant overlap between CT+ and CT+/MG+ women.
Tamarelle et al. [20]	Not reported	Women with confirmed C. trachomatis infection at baseline and after azithromycin treatment at 3, 6 and 9 months (n = 149), and CT negative controls (n = 99).	African-American	Vaginal swabs	V3-4 Illumina	CT women microbiota was dominated, at the time of diagnosis, by L. iners or a diverse array of BV or CST-IV associated bacteria, such as G. vaginalis, A. vaginae and M. curtisii. L. iners-dominated communities were most common after azithromycin treatment (1 g monodose), consistent to the observed relative resistance of this bacterium to azithromycin.
Chen et al. [22]	2019–2020	Women with tubal infertility and C. trachomatis infection before (CT-P, n = 6) and after treatment (CT-PT, n = 4), as compared to infertile (CT-N, n = 8) or healthy women (CT-C, n = 7) without chlamydial infection (controls)	Asian	Vaginal swabs	V3-4 Illumina	Women with tubal infertility and CT presented a L. iners dominated microbiota with a decrease in Lactobacillus, Bifidobacterium, Enterobacter, Atopobium, and Streptococcus spp., which could be restored with varying degrees by azythromycin treatment. C. trachomatis-positive women also had increased levels of IFNγ and IL-10.
Raimondi et al. [23]	2019	Women with contemporary vaginal and ano-rectal C. trachomatis infection (CT-positive, n = 10), and uninfected controls (CT-negative, n = 16).	European	Vaginal and anal swabs	V3-4 Illumina	Alpha-diversity via Pielou’s index was higher in the vaginal microbiota of CT-positive women than CT-negative women. In CT-positive women, the vaginal microbiota was depleted of Lactobacillus spp., with a significant increase in anaerobes, like Sneathia spp., Parvimonas spp., and Megasphaera spp. CT positively correlated with Ezakiella spp. The predicted metabolic functions showed increased chorismate and aromatic amino-acid biosynthesis, as well as mixed acid fermentation, in the vaginal microbiota of CT-positive women.
Chiu et al. [16]	2018–2019	Women with vaginitis and C. trachomatis (CT, n = 22), Trichomonas vaginalis (TV, n = 7), Neisseria gonorrhoeae (GC, n = 2), mixed infections (TV/CT, n = 2; TV/CT/GC, n = 1), as well as uninfected controls (non-STI, n = 36).	Asian	Vaginal swabs	V3-4 Illumina	In CT women, the vaginal microbiota was dominated by L. iners, with increased relative abundance of G. vaginalis as compared to TV and non-STI women. In TV women, Lactobacillus spp. was significantly lower, and S. agalactiae, P. bivia, S. sanguinegens and G. asaccharolytica were significantly enriched, as compared to the other patient groups.